Genomics (ALWAYS UNDER CONSTRUCTION)

BIOL 4400--01 Fall 2023

Syllabus

Learning Objectives

Upon completion of this course, students will be able to:

1. Summarize the subtopics: sequencing methods and strategies, bioinformatics and sequence comparison, sequence alignment and phylogenetic reconstruction,
comparative genomics, organization and structure of genomes, genome annotation, transcriptomics and proteomics

2. Interpret constructed evolutionary trees derived from molecular data.

3. Carry out genomic analyses such as annotation, transcriptomics, functional genomics, metagenomics, and genetic variation and SNPs

4. Employ critical thinking skills in discussions about genomics

Schedule (Subject to Change)

Week Dates Topic Readings Due
1 Aug. 23

Aug. 25		 Intro. & Syllabus

How to read a paper		 For Class:
Various Online articles (see Canvas) 		Pre-course quiz--Aug. 25

Questions about scientific papers--Aug. 25
2 Aug. 28

Aug. 30

Sep. 1		 How to read a paper pt. 2

Overview of genetics and genomics

Structural components of the genome		 For Class:
Various Online articles (see Canvas)		 Discussion signup--Aug. 30
3 Sep. 4

Sep. 6

Sep. 8		 NO CLASS--LABOR DAY

Sanger sequencing and the Human Genome Project

Discussion on HGP		 For Class:
Watson 1990
Bentley 2000

For Discussion:
Nurk et al. 2022		 Selection of Project Subject--Sep. 8

Precis Sep. 8
4 Sep. 11

Sep. 13

Sep. 15		 Human Genome Project

Implications and applications of HGP

Discussion: All of Us Project		 For Class:
Gibbs 2020
Mao and Zhang 2022

For Discussion:
All of Us intro
Ramirez et al. 2022		 Precis Sep 15
5 Sep. 18

Sep. 20

Sep. 22		 Next generation sequencing methods

Third generation sequencing

Discussion Comparing Sequencing Methods
 For Class:
Shendure et al. 2017
Heather and Chain 2016

For Discussion:
Hotaling et al. 2023		 Precis Sep. 22
6 Sep. 25

Sep. 27

Sep. 29		 Output from sequencing methods

Investigate SRA, setup Galaxy Account

Discussion on Galaxy/Open tools		 For Class:
Galaxy 2020

For Discussion
Hiltemann et al. 2023		 Precis Sep. 29
7 Oct. 2

Oct. 4

Oct. 6		 Genome assembly methods

Genome assembly methods

Discussion on Genome Assembly
 For Class:
Rice and Green 2019

For Discussion:
Wick and Holt 2023		 Exam 1 Due Oct. 4

Precis Oct. 6
8 Oct. 9

Oct. 11

Oct. 13		 Genome polishing and annotation

Genome annotation and BUSCO

Discussion on Assessing Genome Quality		 For Class:
Yandell and Ence 2012

For Discussion:
Marks et al. 2021		 Outline and Annotated Bibliography due Oct. 13

Precis Oct. 13
9 Oct. 16

Oct. 18

Oct. 20		 Genome assembly assignment

BUSCO and annotation hands on

FALL BREAK--NO CLASS		 Recommended Reading:
Dunn et al. 2019		 -
10 Oct. 23

Oct. 25

Oct. 27		 Sequence alignments and substitution models

Phylogenetics

Discussion on Phylogenomics		 For Class:
Kapli et al. 2020

For Discussion:
Kawahara et al. 2023		 Hands on Activities due Oct. 25

Precis Oct. 27
11 Oct. 30

Nov. 1

Nov. 3		 Phylogenomics hands on

Phylogenomics Hands on

Phylogenomics		 For Class:
Steenwyk et al. 2023		 Phylogenetics Hands on by Nov. 3

Meet with Dr. Hjelmen by Nov. 3
12 Nov. 6

Nov. 8

Nov. 10		 WORK ON FINAL PROJECT

WORK ON FINAL PROJECT

Discussion on Introgression		 For Discussion:
Koller et al. 2022		 Precis Nov. 10
13 Nov. 13

Nov. 15

Nov. 17		 Comparative Genomics

Interpreting Comparative Genomics Plots

Poster Prep Day		 For Class:
Stephan et al. 2022		 Poster Draft Due Nov. 13

Peer Review for Posters Due Nov. 17
- Nov. 20

Nov. 21

Nov. 24		 THANKSGIVING BREAK--NO CLASS
14 Nov. 27

Nov. 29

Dec. 1		 Poster Prep Day

Population Genomics

Discussion on Comparative Genomics		 For Class:
Webster et al. 2023

For Discussion:
Christmas et al. 2023		 Final Posters Due by Nov. 27

Precis Nov. 17
15 Dec. 4

Dec. 6

Dec. 8		 PRESENT POSTER FINAL

Population Genomics cont.

Discussion on Population Genomics		 For Discussion:
Ragsdale et al. 2023		 Exam 2 due Nov. 17

Precis Dec. 1


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